ajmart.c

Prototype

AjPMartquery ajMartqueryNew (
      void
);

Type Name Read/Write Description

AjPMartquery RETURN Mart query object

Type	Name	Read/Write	Description
`AjPMartquery`		RETURN	Mart query object

From EMBOSS 6.3.0

Prototype

void ajMartqueryDel (
      AjPMartquery* thys
);

Type Name Read/Write Description

AjPMartquery* thys Modify Mary query object

void RETURN

Type	Name	Read/Write	Description
`AjPMartquery*`	`thys`	Modify	Mary query object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartquerySeqinFree

Delete Mart query object given a seqin object

Prototype

void ajMartquerySeqinFree (
      AjPSeqin thys
);

Type Name Read/Write Description

AjPSeqin thys Modify Seqin query object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`thys`	Modify	Seqin query object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartLocNew

Create object for holding Mart location data read from XML

Prototype

AjPMartLoc ajMartLocNew (
      void
);

Type Name Read/Write Description

AjPMartLoc RETURN MartLoc object

Type	Name	Read/Write	Description
`AjPMartLoc`		RETURN	MartLoc object

From EMBOSS 6.3.0

Prototype

void ajMartLocDel (
      AjPMartLoc* thys
);

Type Name Read/Write Description

AjPMartLoc* thys Modify MartLoc object

void RETURN

Type	Name	Read/Write	Description
`AjPMartLoc*`	`thys`	Modify	MartLoc object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartDatasetNew

Create object for holding Mart Dataset read from XML (or tab-sep list)

Prototype

AjPMartDataset ajMartDatasetNew (
      void
);

Type Name Read/Write Description

AjPMartDataset RETURN MartDataset object

Type	Name	Read/Write	Description
`AjPMartDataset`		RETURN	MartDataset object

From EMBOSS 6.3.0

Prototype

void ajMartDatasetDel (
      AjPMartDataset* thys
);

Type Name Read/Write Description

AjPMartDataset* thys Modify MartDataset object

void RETURN

Type	Name	Read/Write	Description
`AjPMartDataset*`	`thys`	Modify	MartDataset object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartAttributeNew

Create object for holding Mart Attributes read from XML (or tab-sep list)

Prototype

AjPMartAttribute ajMartAttributeNew (
      void
);

Type Name Read/Write Description

AjPMartAttribute RETURN MartAttribute object

Type	Name	Read/Write	Description
`AjPMartAttribute`		RETURN	MartAttribute object

From EMBOSS 6.3.0

Prototype

void ajMartAttributeDel (
      AjPMartAttribute* thys
);

Type Name Read/Write Description

AjPMartAttribute* thys Modify MartAttribute object

void RETURN

Type	Name	Read/Write	Description
`AjPMartAttribute*`	`thys`	Modify	MartAttribute object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartFilterNew

Create object for holding Mart Filters read from XML (or tab-sep list)

Prototype

AjPMartFilter ajMartFilterNew (
      void
);

Type Name Read/Write Description

AjPMartFilter RETURN MartFilter object

Type	Name	Read/Write	Description
`AjPMartFilter`		RETURN	MartFilter object

From EMBOSS 6.3.0

Prototype

void ajMartFilterDel (
      AjPMartFilter* thys
);

Type Name Read/Write Description

AjPMartFilter* thys Modify MartFilter object

void RETURN

Type	Name	Read/Write	Description
`AjPMartFilter*`	`thys`	Modify	MartFilter object
`void`		RETURN

From EMBOSS 6.3.0

Prototype

AjPMartdsinfo ajMartDsinfoNew (
      void
);

Type Name Read/Write Description

AjPMartdsinfo RETURN Martdsinfo object

Type	Name	Read/Write	Description
`AjPMartdsinfo`		RETURN	Martdsinfo object

From EMBOSS 6.3.0

Prototype

void ajMartDsinfoDel (
      AjPMartdsinfo* thys
);

Type Name Read/Write Description

AjPMartdsinfo* thys Modify Mart Dsinfo object

void RETURN

Type	Name	Read/Write	Description
`AjPMartdsinfo*`	`thys`	Modify	Mart Dsinfo object
`void`		RETURN

From EMBOSS 6.3.0

Prototype

AjPMartqinfo ajMartQinfoNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input number of datasets

AjPMartqinfo RETURN Martqinfo object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	number of datasets
`AjPMartqinfo`		RETURN	Martqinfo object

From EMBOSS 6.3.0

Prototype

void ajMartQinfoDel (
      AjPMartqinfo* thys
);

Type Name Read/Write Description

AjPMartqinfo* thys Modify Mart Qinfo object

void RETURN

Type	Name	Read/Write	Description
`AjPMartqinfo*`	`thys`	Modify	Mart Qinfo object
`void`		RETURN

From EMBOSS 6.3.0

Prototype

AjBool ajMartregistryParse (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object holding mart info
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Prototype

AjBool ajMartGetRegistry (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetDatasets

Return datasets given a mart registry and a mart name within it

Prototype

AjBool ajMartGetDatasets (
      AjPSeqin seqin,
      const AjPStr mart
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr mart Input "Sequence" mart name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`mart`	Input	"Sequence" mart name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Prototype

AjBool ajMartdatasetParse (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object holding mart info
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartGetAttributes

Return attributes given a mart dataset and a mart host/path/port

Prototype

AjBool ajMartGetAttributes (
      AjPSeqin seqin,
      const AjPStr dataset
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetAttributesRetry

Retry an attribute fetch using the main biomart registry site This routine should only be called after an ajMartGetAttribute call followed by a ajMartattributesParse has returned an error. That typically means that an external server has not provided all the attributes fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

Prototype

AjBool ajMartGetAttributesRetry (
      AjPSeqin seqin,
      const AjPStr dataset
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetAttributesSchema

Return attributes given a mart dataset, a mart host/path/port and a schemaname.

Prototype

AjBool ajMartGetAttributesSchema (
      AjPSeqin seqin,
      const AjPStr dataset,
      const AjPStr schema
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

const AjPStr schema Input Schema name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`const AjPStr`	`schema`	Input	Schema name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartattributesParse

Read a mart attributes buffer

Prototype

AjBool ajMartattributesParse (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object holding mart info
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartGetFilters

Return filters given a mart dataset and a mart host/path/port

Prototype

AjBool ajMartGetFilters (
      AjPSeqin seqin,
      const AjPStr dataset
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetFiltersSchema

Return filters given a mart dataset, a mart host/path/port and a schema

Prototype

AjBool ajMartGetFiltersSchema (
      AjPSeqin seqin,
      const AjPStr dataset,
      const AjPStr schema
);

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`const AjPStr`	`schema`	Input	"Sequence" mart schema name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetFiltersRetry

Retry a filters fetch using the main biomart registry site This routine should only be called after an ajMartGetFilters call followed by a ajMartfiltersParse has returned an error. That typically means that an external server has not provided all the filters fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

Prototype

AjBool ajMartGetFiltersRetry (
      AjPSeqin seqin,
      const AjPStr dataset
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`const AjPStr`	`dataset`	Input	"Sequence" mart dataset name
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartfiltersParse

Parse a mart filters buffer

Prototype

AjBool ajMartfiltersParse (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object holding mart info
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartFilterMatch

Associate filters with a given attribute table

Prototype

AjBool ajMartFilterMatch (
      AjPTable atab,
      const AjPMartFilter filt
);

Type Name Read/Write Description

AjPTable atab Modify Attribute table

const AjPMartFilter filt Input filters

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPTable`	`atab`	Modify	Attribute table
`const AjPMartFilter`	`filt`	Input	filters
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartAssociate

Associate filters with attributes thgat can use them

Prototype

AjBool ajMartAssociate (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object holding mart info
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartMakeQueryXml

Produce XML from an AjPMartqinfo object

Prototype

void ajMartMakeQueryXml (
      const AjPMartqinfo qinfo,
      AjPSeqin seqin
);

Type Name Read/Write Description

const AjPMartqinfo qinfo Input Mart qinfo object

AjPSeqin seqin Modify Seqin object

void RETURN

Type	Name	Read/Write	Description
`const AjPMartqinfo`	`qinfo`	Input	Mart qinfo object
`AjPSeqin`	`seqin`	Modify	Seqin object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartSendQuery

Send a query, given biomart query xml, to a mart server host/path/port

Prototype

AjBool ajMartSendQuery (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

AjBool RETURN true on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	"Sequence" input object
`AjBool`		RETURN	true on success

From EMBOSS 6.3.0

Function ajMartGetReghost

Return the Registry host name

Prototype

const AjPStr ajMartGetReghost (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

const AjPStr RETURN Registry host name or NULL

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`const AjPStr`		RETURN	Registry host name or NULL

From EMBOSS 6.3.0

Function ajMartGetRegpath

Return the Registry path name

Prototype

const AjPStr ajMartGetRegpath (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

const AjPStr RETURN Registry host name or NULL

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`const AjPStr`		RETURN	Registry host name or NULL

From EMBOSS 6.3.0

Function ajMartGetRegport

Return the Registry port

Prototype

ajuint ajMartGetRegport (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

ajuint RETURN Registry port or 0

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`ajuint`		RETURN	Registry port or 0

From EMBOSS 6.3.0

Function ajMartGetMarthost

Return the Mart host name

Prototype

const AjPStr ajMartGetMarthost (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

const AjPStr RETURN Mart host name or NULL

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`const AjPStr`		RETURN	Mart host name or NULL

From EMBOSS 6.3.0

Function ajMartGetMartpath

Return the Mart path name

Prototype

const AjPStr ajMartGetMartpath (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

const AjPStr RETURN Mart host name or NULL

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`const AjPStr`		RETURN	Mart host name or NULL

From EMBOSS 6.3.0

Function ajMartGetMartport

Return the Mart port

Prototype

ajuint ajMartGetMartport (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

ajuint RETURN Mart port or 0

Type	Name	Read/Write	Description
`const AjPSeqin`	`seqin`	Input	Seqin object
`ajuint`		RETURN	Mart port or 0

From EMBOSS 6.3.0

Function ajMartSetReghostC

Set the Registry host name

Prototype

AjBool ajMartSetReghostC (
      AjPSeqin seqin,
      const char* reghost
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const char* reghost Input Registry name

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const char*`	`reghost`	Input	Registry name
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetRegpathC

Return the Registry path name

Prototype

AjBool ajMartSetRegpathC (
      AjPSeqin seqin,
      const char* regpath
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const char* regpath Input Registry path

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const char*`	`regpath`	Input	Registry path
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetReghostS

Set the Registry host name

Prototype

AjBool ajMartSetReghostS (
      AjPSeqin seqin,
      const AjPStr reghost
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const AjPStr reghost Input Registry name

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const AjPStr`	`reghost`	Input	Registry name
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetRegpathS

Return the Registry path name

Prototype

AjBool ajMartSetRegpathS (
      AjPSeqin seqin,
      const AjPStr regpath
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const AjPStr regpath Input Registry path

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const AjPStr`	`regpath`	Input	Registry path
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetRegport

Return the Registry port

Prototype

AjBool ajMartSetRegport (
      AjPSeqin seqin,
      ajuint regport
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

ajuint regport Input Registry port

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`ajuint`	`regport`	Input	Registry port
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetMarthostC

Set the Mart host name

Prototype

AjBool ajMartSetMarthostC (
      AjPSeqin seqin,
      const char* marthost
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const char* marthost Input Mart name

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const char*`	`marthost`	Input	Mart name
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetMartpathC

Set the Mart path name

Prototype

AjBool ajMartSetMartpathC (
      AjPSeqin seqin,
      const char* martpath
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const char* martpath Input Mart path

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const char*`	`martpath`	Input	Mart path
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetMarthostS

Set the Mart host name

Prototype

AjBool ajMartSetMarthostS (
      AjPSeqin seqin,
      const AjPStr marthost
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const AjPStr marthost Input Mart name

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const AjPStr`	`marthost`	Input	Mart name
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetMartpathS

Set the Mart path name

Prototype

AjBool ajMartSetMartpathS (
      AjPSeqin seqin,
      const AjPStr martpath
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

const AjPStr martpath Input Mart path

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`const AjPStr`	`martpath`	Input	Mart path
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartSetMartport

Set the Mart port

Prototype

AjBool ajMartSetMartport (
      AjPSeqin seqin,
      ajuint martport
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

ajuint martport Input Mart port

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`ajuint`	`martport`	Input	Mart port
`AjBool`		RETURN	True on success

From EMBOSS 6.3.0

Function ajMartFixRegistry

Try to fill in missing registry fields

Prototype

void ajMartFixRegistry (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartFixMart

Try to fill in missing mart fields

Prototype

void ajMartFixMart (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

void RETURN True if valid

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`void`		RETURN	True if valid

From EMBOSS 6.3.0

Function ajMartAttachMartquery

Add a mart query object to a seqin object

Prototype

void ajMartAttachMartquery (
      AjPSeqin seqin,
      AjPMartquery mq
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

AjPMartquery mq Modify Martquery object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Seqin object
`AjPMartquery`	`mq`	Modify	Martquery object
`void`		RETURN

From EMBOSS 6.3.0

Function ajMartGetMartqueryPtr

Return a seqin Query pointer

Prototype

AjPMartquery ajMartGetMartqueryPtr (
      const AjPSeqin seqin
);

Type Name Read/Write Description

const AjPSeqin seqin Input Seqin object

AjPMartquery RETURN Martquery

From EMBOSS 6.3.0

Function ajStrtokQuotR

Reentrant strtok that disallows tokenisation at delimiter characters if they are within quotation chracters e.g. tokenisation of -token1="a,b,c",-token2 will yield -token1="a,b,c" and -token2 if the delimstr contains ',' and the quotstr contains '"'

Prototype

char* ajStrtokQuotR (
      const char* srcstr,
      const char* delimstr,
      const char* quotstr,
      const char** ptrptr,
      AjPStr* buf
);

Type Name Read/Write Description

const char* srcstr Input Source string

const char* delimstr Input Delimiter string

const char* quotstr Input Allowable quotes(s)

const char** ptrptr Input Saved position in srcstr

AjPStr* buf Output Results buffer (the token)

char* RETURN Pointer to start of token (in buf) or NULL

From EMBOSS 6.3.0

Function ajMartParseParameters

Parses attribute and filter strings and load a given Qinfo object with them

Prototype

AjBool ajMartParseParameters (
      AjPMartqinfo qinfo,
      const AjPStr atts,
      const AjPStr filts,
      ajuint idx
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Query object

const AjPStr atts Input Attributes

const AjPStr filts Input Filters

ajuint idx Input dataset index

AjBool RETURN False on parsing or loading error

From EMBOSS 6.3.0

Function ajMartSetQuerySchemaC

Set the Qinfo Virtual Schema field

Prototype

void ajMartSetQuerySchemaC (
      AjPMartqinfo qinfo,
      const char* schema
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

const char* schema Input Virtual schema

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryVersionC

Set the Qinfo Software Version field

Prototype

void ajMartSetQueryVersionC (
      AjPMartqinfo qinfo,
      const char* version
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

const char* version Input Version

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryFormatC

Set the Qinfo Format field

Prototype

void ajMartSetQueryFormatC (
      AjPMartqinfo qinfo,
      const char* format
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

const char* format Input Format

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryCount

Set the Qinfo Count (unique ID count only) field

Prototype

void ajMartSetQueryCount (
      AjPMartqinfo qinfo,
      AjBool count
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

AjBool count Input count

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryHeader

Set the Qinfo Header (column title) field

Prototype

void ajMartSetQueryHeader (
      AjPMartqinfo qinfo,
      AjBool header
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

AjBool header Input Header

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryUnique

Set the Qinfo Unique rows field

Prototype

void ajMartSetQueryUnique (
      AjPMartqinfo qinfo,
      AjBool unique
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

AjBool unique Input Unique

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryStamp

Set the Qinfo Completion Stamp ([success]) field

Prototype

void ajMartSetQueryStamp (
      AjPMartqinfo qinfo,
      AjBool stamp
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

AjBool stamp Input Stamp

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryVerify

Set the Qinfo verification field to test that given atts & filts exist in the dataset

Prototype

void ajMartSetQueryVerify (
      AjPMartqinfo qinfo,
      AjBool verify
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

AjBool verify Input verify flag

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryDatasetName

Set a Qinfo dataset name field

Prototype

void ajMartSetQueryDatasetName (
      AjPMartqinfo qinfo,
      const AjPStr name,
      ajuint idx
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

const AjPStr name Input Name

ajuint idx Input Dataset number (0->n-1)

void RETURN

From EMBOSS 6.3.0

Function ajMartSetQueryDatasetInterfaceC

Set a Qinfo dataset interface field

Prototype

void ajMartSetQueryDatasetInterfaceC (
      AjPMartqinfo qinfo,
      const char* iface,
      ajuint idx
);

Type Name Read/Write Description

AjPMartqinfo qinfo Modify Seqin object

const char* iface Input Interface

ajuint idx Input Dataset number (0->n-1)

void RETURN

From EMBOSS 6.3.0

Function ajMartCheckQinfo

Try to fill in missing fields and check user attributes/filters

Prototype

AjBool ajMartCheckQinfo (
      AjPSeqin seqin,
      AjPMartqinfo qinfo
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

AjPMartqinfo qinfo Modify Mart qinfo object

AjBool RETURN True if valid

From EMBOSS 6.3.0

Function ajMartGetConfiguration

Return config info given a mart dataset and a mart host/path/port

Prototype

AjBool ajMartGetConfiguration (
      AjPSeqin seqin,
      const AjPStr dataset
);

Type Name Read/Write Description

AjPSeqin seqin Modify "Sequence" input object

const AjPStr dataset Input "Sequence" mart dataset name

AjBool RETURN true on success

From EMBOSS 6.3.0

Function ajMartconfigurationParse

Parse a mart configuration buffer

Prototype

AjBool ajMartconfigurationParse (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding mart info

AjBool RETURN True on success

From EMBOSS 6.3.0

Function ajMartattributesPageSort

Sort attributes based on page name

Prototype

AjBool ajMartattributesPageSort (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object holding attribute info

AjBool RETURN True on success

From EMBOSS 6.3.0

Function ajMartNameIsNucC

Test whether name matches any of the set of known nucleic acid biomart terms

Prototype

AjBool ajMartNameIsNucC (
      const char* name
);

Type Name Read/Write Description

const char* name Input Name

AjBool RETURN True if nucleic acid name match

From EMBOSS 6.3.0

Function ajMartNameIsProtC

Test whether name matches any of the set of known protein biomart terms

Prototype

AjBool ajMartNameIsProtC (
      const char* name
);

Type Name Read/Write Description

const char* name Input Name

AjBool RETURN True if nucleic acid name match

From EMBOSS 6.3.0

Function ajMartTableNameIsNuc

Test whether table 'name' value matches any of the set of known nucleic acid biomart terms

Prototype

AjBool ajMartTableNameIsNuc (
      const AjPTable t
);

Type Name Read/Write Description

const AjPTable t Input Table

AjBool RETURN True if nucleic acid name match

From EMBOSS 6.3.0

Function ajMartTableNameIsProt

Test whether table 'name' value matches any of the set of known protein biomart terms

Prototype

AjBool ajMartTableNameIsProt (
      const AjPTable t
);

Type Name Read/Write Description

const AjPTable t Input Table

AjBool RETURN True if protein name match

From EMBOSS 6.3.0

Function ajMartCheckHeader

Return an array of attribute names in the order in which they are returned by the biomart server. Requires that the header flag was set and that an attribute query has previously loaded to MartAttribute field.

Prototype

AjPStr* ajMartCheckHeader (
      AjPSeqin seqin,
      AjPMartqinfo qinfo
);

Type Name Read/Write Description

AjPSeqin seqin Modify Seqin object

AjPMartqinfo qinfo Modify Mart qinfo object

AjPStr* RETURN Array of attribute names terminated by a NULL entry. or NULL if mapping cannot be done

From EMBOSS 6.3.0

Function ajMartDecodeHname

Decode directory name into host/path/port

Prototype

void ajMartDecodeHname (
      const AjPStr dir,
      AjPStr* host,
      AjPStr* path,
      ajuint* port
);

Type Name Read/Write Description

const AjPStr dir Input Encoded directory name

AjPStr* host Output Host

AjPStr* path Output Path

ajuint* port Output Port

void RETURN

From EMBOSS 6.4.0

Type	Name	Read/Write	Description
`const char*`	`srcstr`	Input	Source string
`const char*`	`delimstr`	Input	Delimiter string
`const char*`	`quotstr`	Input	Allowable quotes(s)
`const char**`	`ptrptr`	Input	Saved position in srcstr
`AjPStr*`	`buf`	Output	Results buffer (the token)
`char*`		RETURN	Pointer to start of token (in buf) or NULL

Type	Name	Read/Write	Description
`const char*`	`name`	Input	Name
`AjBool`		RETURN	True if nucleic acid name match

Type	Name	Read/Write	Description
`const AjPTable`	`t`	Input	Table
`AjBool`		RETURN	True if nucleic acid name match

Type	Name	Read/Write	Description
`const AjPStr`	`dir`	Input	Encoded directory name
`AjPStr*`	`host`	Output	Host
`AjPStr*`	`path`	Output	Path
`ajuint*`	`port`	Output	Port
`void`		RETURN